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HOOMD


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OS: Linux, Windows, Mac, ...

License: Freeware

Methods: MM, MD



HOOMD-blue stands for Highly Optimized Object-oriented Many-particle Dynamics -- Blue Edition. It performs general purpose particle dynamics simulations on a single workstation, taking advantage of NVIDIA GPUs to attain a level of performance equivalent to dozens of processor cores on a fast cluster.

The object oriented design of HOOMD-blue makes it versatile and expandable. A number of different force fields and integrators are present in the current version, and additional ones can be added easily.

Simulations are configured and run using simple python scripts, allowing complete control over the force field choice, integrator, all parameters, how many time steps are run, etc... . The scripting system is designed to be as simple as possible to the non-programmer. History

HOOMD-blue is a direct continuation of the project HOOMD, originally developed at Ames Lab and Iowa State University: http://www.ameslab.gov/hoomd. The HOOMD-blue lead development effort is at the University of Michigan, though we of course have many contributors from around the world. The "blue" suffix is actually part of the acronym and stands for Blue Edition, a subtle hint to one of the Michigan school colors.

Features:

Executes particle dynamics simulations on NVIDIA GPUs with the same performance as a cluster of CPUs
Supports Windows, Linux, and Mac OS X

Pair Potentials
Lennard-Jones
Gaussian
CGCMM

Bond Potentials
FENE
Harmonic

Angle Potentials
Harmonic
CGCMM

Dihedral/Improper Potentials
Harmonic

Wall Potentials
Lennard-Jones

Integrators
Brownian dynamics NVT
NPT
NVE
NVT

Dump file formats
HOOMD's XML input format
MOL2
DCD
PDB

Large simulations can be run on multiple GPUs in a single host
Simple, but powerful, script interface for defining simulations
Advanced built-in initial configuration generators
Human readable XML input files
Space-filling curve particle reordering to increase performance
Extensible object-oriented design, so adding additional potentials and integrators is straightforward.
Simulations can be visualized in real-time using VMD's IMD interface.
Pair potentials and forces can be varied smoothly to 0 at the cutoff
Real time analysis can be run at a non-linear rate if desired
Quantities such as temperature, pressure, and box size can be varied smoothly over a run

http://codeblue.umich.edu/hoomd-blue/



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